Biology subjects

Sun, S.

Publications and source records attributed to Sun, S..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Arabidopsis root lipid droplets are hubs for membrane homeostasis under heat stress, and triterpenoid synthesis and storage.

O_LIPlant lipid droplets (LDs) and their associated proteins have numerous subcellular and physiological functions. While considerable progress has been made for LDs in many tissues, the function and composition of LDs in roots remains largely unexplored. C_LIO_LIWe investigated the changes of the number of LDs and of the lipidome in heat-stressed Arabidopsis thaliana roots. Furthermore, we isolated root LDs from the Arabidopsis mutant trigalactosyldiacylglycerol 1-1 sugar dependent 1-4 and investigated their proteome and lipidome. C_LIO_LIHeat stress lead to a degradation of membrane lipids and an increase in TAGs and LDs. while, fatty acid SEs decreased, probably acting as precursors for acylated sterol glycosides. A variety of proteins were enriched in root LDs, which are thus far not described as LD proteins. Transient expression of these proteins in many cases confirmed their LD localization, for example of the triterpene biosynthetic enzymes thalianol synthase and marneral synthase. We could furthermore show that the educts and products of these enzymes are enriched in root LDs, too. C_LIO_LIWe conclude that root LDs simultaneously act as a sink and source during heat stress-induced membrane remodeling. Furthermore, root LDs play a pivotal role in triperpene synthesis and storage, thereby highlighting LDs as hubs in specialized metabolism. C_LI

plant biology↗

bioRxiv2025

Leveraging mRNA platform for the development of vaccines against egg allergy

Food allergy has posed a major global health burden due to the rising prevalence and lack of effective prophylactic strategies. During the past decades, allergen-specific immunotherapy (AIT) has been used as a disease-modifying therapy for food allergic conditions, but due to the long-term treatment duration, poor patient compliance and unexpected adverse reactions, only a minority of patients benefit from AIT therapy. In this proof-of-concept study, using well-established mRNA platform, we developed mRNA vaccine candidates encoding for the major egg white allergen Gal d2 (also known as ovalbumin) and comprehensively evaluated the prophylactic efficacy against anaphylaxis in a Gal d2-induced allergic mouse model. Two vaccine formulations, Gal d2 mRNA vaccine and Gal d2-IL-10 mRNA vaccine, both demonstrated effective ability in preventing the onset of allergic disease, which is largely attributed to the versatilities of mRNA vaccine in eliciting allergen-blocking antibody, shifting Th2 towards Th1 immunity, as well as in generating peripheral tolerance.

immunology↗

bioRxiv2025

Cocktail Chemical Labeling for In-Depth Surfaceome Profiling of Bone-Marrow Derived Dendritic Cells

Cell surface proteins (CSPs) are crucial identifiers for cell types and states, especially in dendritic cells (DCs). Current proteomic methods for profiling CSPs are limited by their hydrophobic nature and low abundance, which often require genetic or cell surface engineering and exhibit biased and insufficient labeling efficiency. Herein, we report [Ru(bpy)3]Cl2 (Ru) for effective biotinylation on the cell surfaceome via a simple "mix and lighten" method. The versatile photoredox pathways of Ru are leveraged using a probe cocktail of biotin-phenol and biotin-hydrazide for improved substrate coverage. The "cocktail" labeling strategy results in reproducible identification of up to 733 plasma membrane proteins on HeLa cells, and is further applied to map dynamic changes in the surfaceome during the differentiation of primary bone marrow-derived dendritic cells, which demonstrates a user-friendly and deep-surfaceome-coverage tool for profiling dynamic changes in primary cells, with potential implications for cell identities, functional states, and novel drug targets.

cell biology↗

bioRxiv2025

KSHV Reprograms Host RNA Splicing via FAM50A to Activate STAT3 and Drive Oncogenic Cellular Transformation

RNA alternative splicing is a fundamental cellular process implicated in cancer development. Kaposis sarcoma-associated herpesvirus (KSHV), the etiological agent of multiple human malignancies, including Kaposis sarcoma (KS), remains a significant concern, particularly in AIDS patients. A CRISPR-Cas9 screening of matched primary rat mesenchymal stem cells (MM) and KSHV-transformed MM cells (KMM) identified key splicing factors involved in KSHV-induced cellular transformation. To elucidate the mechanisms by which KSHV-driven splicing reprogramming mediates cellular transformation, we performed transcriptomic sequencing, identifying 131 differential alternative splicing transcripts, with exon skipping as the predominant event. Notably, these transcripts were enriched in vascular permeability, multiple metabolic pathways and ERK1/2 signaling cascades, which play key roles in KSHV-induced oncogenesis. Further analyses of cells infected with KSHV mutants lacking latent genes including vFLIP, vCyclin and viral miRNAs, as well as cells overexpressing LANA, revealed their involvement in alternative splicing regulation. Among the identified splicing factors, FAM50A, a component of the spliceosome complex C, was found to be crucial for KSHV-mediated transformation. FAM50A knockout resulted in distinct splicing profiles in both MM and KMM cells, and significantly inhibited KSHV-driven proliferation, cellular transformation and tumorigenesis. Mechanistically, FAM50A knockout altered SHP2 splicing, promoting an isoform with enhanced enzymatic activity that led to reduced STAT3 Y705 phosphorylation in KMM cells. These findings reveal a novel paradigm in which KSHV hijacks host splicing machinery, specifically FAM50A-mediated SHP2 splicing, to sustain STAT3 activation and drive oncogenic transformation. ImportanceKaposis sarcoma-associated herpesvirus (KSHV) causes cancers such as Kaposis sarcoma, particularly in AIDS patients. This study uncovers how KSHV hijacks a fundamental cellular process called RNA splicing to promote cancer development. We identified key splicing events that alter critical pathways involved in vascular permeability, metabolism, and oncogenic signaling, particularly ERK1/2 and STAT3. A specific protein, FAM50A, was found to be essential for KSHV-driven cancerous transformation. Removing FAM50A disrupted splicing, weakening cancer-promoting signals. These findings provide new insights into how viruses manipulate host cells to drive cancer and highlight RNA splicing as a potential target for future therapies.

cancer biology↗

bioRxiv2025

Deciphering Ibogaines Matrix Pharmacology: Multiple Transporter Modulation at Serotonin Synapses

Ibogaine is the main psychoactive alkaloid produced by the iboga tree (Tabernanthe iboga) that has a unique therapeutic potential across multiple indications, including opioid dependence, substance use disorders, depression, anxiety, posttraumatic stress disorder (PTSD), and traumatic brain injury (TBI). We systematically examined the effects of ibogaine, its main metabolite noribogaine, and a series of iboga analogs at monoamine neurotransmitter transporters, some which have been linked to the oneiric and therapeutic effects of these substances. We report that ibogaine and noribogaine inhibit the transport function of the vesicular monoamine transporter 2 (VMAT2) with sub-micromolar potency in cell-based fluorimetry assays and at individual synaptic vesicle clusters in mouse brain as demonstrated via two-photon microscopy. The iboga compounds also inhibit the plasma membrane monoamine transporters (MATs), prominently including the serotonin transporter (SERT), and a novel iboga target, the organic cation transporter 2 (OCT2). SERT transport inhibition was demonstrated in serotonin axons and soma in the brain and in rat brain synaptosomes, where ibogaine and its analogs did not act as substrate-type serotonin releasers. Noribogaine showed dual inhibition of VMAT2 and SERT with comparable potency, providing an explanatory model for the known neurochemical effects of ibogaine in rodents. Together, the updated profile of the monoamine transporter modulation offers insight into the complexity of the iboga pharmacology, which we termed "matrix pharmacology". The matrix pharmacology concept is outlined and used to explain why ibogaine and noribogaine do not induce catalepsy, as demonstrated in our study, in contrast to other VMAT2 inhibitors. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/641351v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@a1cacaorg.highwire.dtl.DTLVardef@8be27org.highwire.dtl.DTLVardef@1fc320forg.highwire.dtl.DTLVardef@3a8837_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

A potent and selective TNKS2 inhibitor for tumor-selective WNT suppression

Hyperactive WNT signaling is a potent cancer driver, but clinical translation of WNT inhibitors has been hampered by on-target toxicities. WNT signaling can be constrained through inhibition of the PARP family enzymes Tankyrase 1 (TNKS1) and Tankyrase 2 (TNKS2), however, existing TNKS inhibitors suppress WNT signaling in both tumor and healthy tissues. In this study, we show that the loss of chromosome 8p that occurs in approximately half of advanced epithelial malignancies, creates a collateral vulnerability that enables tumor-selective inhibition of Tankyrase activity. 8p loss depletes expression of TNKS1 and creates a tumor-specific dependency on the functionally redundant TNKS2 protein. Through structure-guided drug design, we identify a first-in-class TNKS2-selective inhibitor that can drive selective WNT inhibition in TNKS1-deficient oncogenic cell and organoid models. This work demonstrates a targetable vulnerability in multiple cancer types, providing a new approach to potent and selective WNT-targeted therapies.

cancer biology↗

bioRxiv2025

Phagosome-mediated anti-bacterial immunity is governed by the proton-activated chloride channel in peritoneal macrophages

The success of phagosome degradation relies on the ability of phagocytes to regulate the maturation of phagosomes. However, its underlying molecular mechanisms remain poorly understood. Here, we identify the proton-activated chloride (PAC) channel as a key negative regulator of phagosome maturation. PAC deletion enhanced phagosomal acidification and protease activities, leading to augmented bacterial killing in large peritoneal macrophages (LPMs) upon Escherichia coli infection in mice. Surprisingly, phagosome degradation also stimulated STING-IRF3-interferon responses and inflammasome activation in LPMs, both of which are enhanced upon PAC deletion. The increased inflammasome activation induced the release of cleaved gasdermin D, which localized to the surface of bacteria in the peritoneum and further contributed to their killing. Finally, enhanced bacterial clearance by PAC-deficient LPMs reduced proinflammatory immune cell infiltration and peritoneal inflammation, resulting in improved survival in mice. Our study thus provides new insights into the molecular mechanism of phagosome maturation and the dynamics of host defense response following phagosome-mediated bacterial degradation in peritoneal macrophages. SummaryThe PAC channel mediates phagosome maturation during bacterial infection in macrophages. PAC deletion promotes phagosome-mediated STING-interferon signaling and inflammasome-mediated gasdermin D secretion during bacterial infection in peritoneal macrophages.

immunology↗

bioRxiv2025

Intraguild parasitism promotes the persistence of facultative hyperparasitoids by extending temporal host availability

Intraguild predation (IGP) is pervasive in natural food webs, although theoretical models predict restricted parameter space for the coexistence of IG-prey and IG-predators. One potential mechanism is that IGP persistence might be increased when IG-prey extend resource availability for IG-predators. Here we test this hypothesis using manipulative experiments in combination with mathematical modeling. Our experiment system includes Drosophila flies (Drosophila melanogaster, basal resources), primary larval parasitoids (Asobara leveri, IG-prey) and facultative pupal hyperparasitoid (Pachycrepoideus vindemiae, IG-predator). We measured the performance of facultative pupal parasitoids with and without the primary larval parasitoid. Our study revealed that larval parasitoids significantly increased the number of pupal parasitoids emerged from limited host resources, due to the extended resource availability to facultative hyperparasitoid. Specifically, immature primary parasitoids within Drosophila pupae can be explored by facultative hyperparasitoids for up to 14 days, while the healthy fly pupae are available to hyperparasitoids for only 5 days. Despite a significant reduction in offspring fitness of the facultative hyperparasitoids when reared on larval parasitoids versus healthy Drosophila pupae, adult female facultative hyperparasitoids showed no significant preference for healthy fly pupae over immature primary parasitoids. Our theoretical models demonstrated that an extended development period of the primary parasitoid can promote the persistence of the facultative hyperparasitoids and allow their coexistence with the primary parasitoid, although too prolonged development could drive the extinction of the primary parasitoid. As IG-prey often take longer time to develop after consuming the shared resources, extension of temporal resource availability could be a general mechanism contribute to the persistence of intraguild predators. Open research statementData are not yet available, but all of the original experimental data has been displayed in figures 2[~]4. The data will be made publicly available upon manuscript acceptance and archived in the Dryad Digital Repository.

ecology↗

bioRxiv2025

A piece of evidence for pathogenesis of cerebral small vessel disease caused by blood-brain barrier dysfunction

BackgroundBlood-brain barrier (BBB) dysfunction caused by endothelial cell injury is one of the widely accepted pathogenesis of small cerebral vessel disease (CSVD). However, the early microcirculation studies were notably deficient in providing compelling imaging evidence, which has hampered a comprehensive understanding of the pathophysiological processes underlying BBB dysfunction in CSVD. The onset of CSVD is insidious and the clinical manifestations are diverse, diagnosis of CSVD relies primarily on neuroimaging information currently. These MRI imaging features mainly represent the end-stage brain parenchyma injury, rather than the vascular lesion itself. Therefore, clarifying the pathophysiological processes related to cerebral microcirculation in CSVD is of great significance for early treatment intervention of CSVD. MethodsTwenty rats were used to prepare CSVD animal model by ultrasound combined with ultrasonic microbubble contrast agent. MRI, functional ultrasound (fUS) imaging and ultrasound localization microscopy (ULM) were used to evaluate microcirculation changes in acute and chronic models. ResultsCurrently, our research has successfully validated that the imaging characteristics of this model align with the four established criteria outlined in the STRIVE-2 classification. FUS shows increased microflow velocity in the molding area, which can be used for initial evaluation of CSVD models in the acute phase. ULM has revealed a progressive reduction in the density of both the short cortical arteries and the long medullary arteries, along with their respective branches, over time. Concurrently, there has been a noted deviation in blood flow velocity. ConclusionThis model offers compelling evidence at the microvascular level, suggesting that blood-brain barrier (BBB) dysfunction is a central pathophysiological mechanism in the etiology of CSVD. Then it provides a straightforward, efficient, and widely applicable tool and continuous monitoring method for the further investigation of CSVD from the macroscopic to the microscopic circulation level, with significant long-term implications for CSVD diagnosis and treatment.

neuroscience↗

bioRxiv2025

Tracing the evolution and genomic dynamics of mating-type loci in Cryptococcus pathogens and closely related species

Sexual reproduction in basidiomycete fungi is governed by MAT loci (P/R and HD), which exhibit remarkable evolutionary plasticity, characterized by expansions, rearrangements, and gene losses often associated with mating system transitions. The sister genera Cryptococcus and Kwoniella provide a powerful framework for studying MAT loci evolution owing to their diverse reproductive strategies and distinct architectures, spanning bipolar and tetrapolar systems with either linked or unlinked MAT loci. Building on recent comparative genomic analyses, we generated additional chromosome-level assemblies, uncovering distinct trajectories shaping MAT loci organization. Contrasting with the small-scale expansions and gene acquisitions observed in Kwoniella, our analyses revealed independent expansions of the P/R locus in tetrapolar Cryptococcus, possibly driven by pheromone gene duplications. Notably, these expansions coincided with a pronounced GC-content reduction best explained by reduced GC-biased gene conversion following recombination suppression, rather than relaxed codon usage selection. Diverse modes of MAT locus linkage were also identified, including three previously unrecognized transitions: one resulting in a pseudobipolar arrangement and two leading to bipolarity. All three transitions involved translocations. In the pseudobipolar configuration, the P/R and HD loci remained on the same chromosome but genetically unlinked, whereas the bipolar transitions additionally featured rearrangements that fused the two loci into a nonrecombining region. Mating assays confirmed a sexual cycle in C. decagattii, demonstrating its ability to undergo mating and sporulation. Progeny analysis in K. mangrovensis revealed substantial ploidy variation and aneuploidy, likely stemming from haploid-diploid mating, yet evidence of recombination and loss of heterozygosity indicates that meiotic exchange occurs despite irregular chromosome segregation. Our findings underscore the importance of continued diversity sampling and provide further evidence for convergent evolution of fused MAT loci in basidiomycetes, offering new insights into the genetic and chromosomal changes driving reproductive transitions.

genetics↗

bioRxiv2025

The membrane skeleton density of red blood cells in MYH9-related disease patients is decreased

MYH9-related disease (MYH9-RD) is a rare autosomal dominant disorder caused by mutations in MYH9 gene, which encodes the heavy chain of nonmuscle myosin IIA. Nearly all MYH9-RD patients present with macrothrombocytopenia, characterized by decreased platelet count and increased platelet size. In this study, we collected blood samples from three MYH9-RD patients (R702S, D1424N, and R1464C) and unexpectedly found that the actin levels in the red blood cells (RBCs) from all three MYH9-RD patients are substantially lower than the healthy controls. We further revealed that the levels of two RBC membrane skeleton proteins, -spectrin and tropomodulin, are also reduced in MYH9-RD RBCs. We showed that the membrane skeleton of MYH9-RD RBCs was more porous and that MYH9-RD RBCs produced more severe deformation under hyperosmotic pressure compared to healthy controls. We conclude that MYH9-RD mutations reduce the RBC membrane skeleton density and impair its mechanical properties, and propose that defects in the membrane skeleton network in RBCs may be a common symptom in MYH9-RD. Key pointsThe levels of membrane skeleton proteins and the density of membrane skeleton network in RBCs of MYH9-RD patients are reduced. MYH9-RD RBCs produce greater deformation under hypertonic conditions compared to healthy controls.

pathology↗

bioRxiv2025

Homeodomain protein Sxi1α regulates cell-cell fusion during distinct sexual reproduction modes in Cryptococcus deneoformans

Sex-specific homeodomain (HD) proteins are key regulators of cell identity and sexual development in fungi, typically functioning as heterodimers to govern transcription. In the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans, the HD proteins Sxi1 and Sxi2a (Sex-inducer 1 and 2a) have been characterized as interacting components that play critical roles in sexual development during x a sexual reproduction. cells are the predominant mating type in natural populations of Cryptococcus, and unisexual (same-sex) mating can also occur in certain genetic backgrounds. The roles of Sxi1 and Sxi2a in unisexual reproduction are not fully understood. To elucidate the functions of Sxi1 and Sxi2a, we first applied AlphaFold3 prediction, which identified potential heterodimeric and homodimeric complexes. Formation of a Sxi2a homodimer was then experimentally validated through yeast two-hybrid assays. We subsequently deleted SXI1 and SXI2a in the hyper-filamentous self-fertile C. deneoformans strains XL280 and XL280a. Disruption of these genes did not result in noticeable defects in vegetative growth, virulence-associated traits, colony morphology, sporulation, or competitive fitness during unisexual crosses. Interestingly, both bilateral (mutant x mutant) and unilateral (mutant x wildtype) crosses involving the sxi1{Delta} mutant significantly increased - cell fusion efficiency, suggesting a previously unrecognized inhibitory role for Sxi1 in regulating same-sex cell fusion. Consistently, genes encoding mating pheromones and the -pheromone receptor Ste3 were upregulated in the sxi1{Delta} fusion assays. Transcriptomic analysis of sxi1{Delta} and sxi2a{Delta} mutants led to the identification of unique subsets of genes negatively regulated by each transcription factor during unisexual reproduction. Additionally, x a crosses between null mutants of sxi1{Delta} and sxi2a{Delta} revealed differential regulation of mating-type (MAT) loci genes dependent only on Sxi1 or Sxi2a. Together, our findings reveal a novel role for Sxi1 in governing cell fusion and demonstrate that Sxi1 and Sxi2a have distinct transcriptional control during unisexual and x a sexual reproduction, potentially exerting opposing regulation of sex-specific MAT genes. Author SummaryAnalogous to processes observed in many eukaryotic organisms, fungal sexual reproduction reshuffles genetic material, producing novel genetic variants with increased fitness and/or adaptive potential. The human fungal pathogen Cryptococcus deneoformans is widespread in the environment and can cause severe infections in immunocompromised individuals. Sexual reproduction in this species occurs between cells of either opposite mating types ( x a mating) or the same mating type ( x and a x a unisexual reproduction). The mating type-specific homeodomain transcription factors Sxi1 and Sxi2a are known to form a complex that broadly controls sexual development following and a cell fusion. Here, we find that Sxi1 inhibits cell-cell fusion during unisexual reproduction, while its partner, Sxi2a, shows only limited inhibition in certain genetic contexts. Further, we show that Sxi1 and Sxi2a regulate transcription of distinct gene sets during both x a and unisexual reproduction, including many within the mating-type (MAT) loci, often in opposing manners. Together, these findings reveal that Sxi1 and Sxi2a function both cooperatively and independently, thereby allowing for a more flexible and finely-tuned mating control system than previously recognized, providing insight into how this organism generates genetic variation and adapts to changing environments.

microbiology↗

bioRxiv2025

Estimating the effect of tissue- and blood-derived cell reference matrices on deconvolving bulk transcriptomic datasets

BackgroundCell deconvolution is a method used to characterize the composition of the mixed cell population in bulk transcriptomic datasets. Tissue- and blood-derived cell reference matrices (CRMs) are typically used, but their impact on deconvolution has yet to be evaluated. MethodsRecursive feature elimination and random forest methods were applied to build tissue- and blood-derived CRMs using single-cell RNA sequencing (scRNA-seq) datasets of inflammatory bowel disease (IBD) which comprises two subtypes (Crohns disease (CD) and ulcerative colitis (UC)). Combining with three published blood-derived CRMs (IRIS, LM22, and ImmunoStates), public bulk transcriptomes datasets and simulated datasets generated from scRNA-Seq were used to evaluate the deconvolution performance by goodness-of-fit and cell fractions correlation. Additionally, two infliximab-treated bulk datasets were used to compare the treatment-related cell types revealed by tissue- and blood-derived CRMs. Lung adenocarcinoma (LUAD) single-cell and TCGA bulk transcriptomic datasets were also used for evaluation. ResultsFor CD and UC tissue bulk datasets, tissue-derived CRMs showed better deconvolution goodness-of-fit scores compared to blood-derived CRMs. Meanwhile, tissue-derived CRMs represented more accurate cellular proportion estimates for most cell types, such as immune and stromal cells in tissue pseudobulk datasets. They also revealed more treatment-related cell types. Additionally, CRMs derived from the scRNA-seq datasets from CD and UC colon samples had similar performance. In contrast, CRMs derived from CD ileum scRNA-seq dataset had better performance in the ileum bulk datasets. All CRMs yielded consistent deconvolution performance when deconvolving blood bulk transcriptomics. The similar results have also been shown using LUAD datasets. ConclusionsOur results emphasize the importance of selecting appropriate CRMs for cell deconvolution, particularly in bulk tissue transcriptomes in immunology and oncology. Such considerations can be extended to encompass other disease implications. AbbVie Disclosure statementAll authors are current employees of AbbVie. The design, study conduct, and financial support for this research were provided by AbbVie. AbbVie participated in the interpretation of data, review, and approval of the publication. Key PointsO_LITissue-derived CRMs showed higher goodness-of-fit compared to blood-derived CRMs for deconvolving bulk tissue transcriptomics. C_LIO_LIAll CRMs yield consistent goodness-of-fit for deconvolving bulk blood transcriptomics. C_LIO_LITissue-derived CRMs represent more accurate cellular proportion estimates and reveal more treatment-related cell types, and the specific tissue type is relevant to the deconvolution performance. C_LI

bioinformatics↗

bioRxiv2025

PSI Atlas: a comprehensive knowledgebase of plant self-incompatibility

Self-incompatibility (SI) is an important genetic mechanism in angiosperms that prevents inbreeding and promotes outcrossing. Although significant progress has been made in understanding SI, its molecular underpinnings and evolutionary origins remain elusive in many plant families. In eudicots, SI is typically regulated by a single S-locus with diverse S-haplotypes, while in grasses, it is controlled by two separate S and Z loci. Genome assemblies of SI plants have greatly facilitated the identification and evolutionary analysis of S-loci. However, a comprehensive database that integrates information on the diverse S-loci has been lacking. To fill this gap, we create the Plant Self-Incompatibility Atlas (PSIA, http://www.plantsi.cn), a knowledgebase that offers an extensive compilation of plant SI, including genomic resources for assembled SI species, the origins and evolution of S genes, and the molecular mechanisms of the eight known SI types. In our most recent release, we have obtained more than 500 genome assemblies across 469 SI species. We have also collected 1275 nucleotide and 1130 protein sequence accessions of S genes from public databases, with a total of 3095 S genes manually identified and curated. PSIA not only thoroughly explores the S-locus information of the assembled SI species but also enables users to efficiently browse, perform BLAST searches, analyze, and download S genes. Additionally, PSIA acts as a comprehensive platform for comparative genomic studies of S-loci, aiding in the exploration of the dynamic processes involved in the origin, loss, and regain of SI. Consequently, PSIA is poised to significantly enhance our understanding of angiosperm SI and offer new perspectives on plant mating systems.

plant biology↗

bioRxiv2025

PROTAC molecule-mediated SpCas9 protein degradation for precise genome editing

CRISPR (clustered regularly interspaced short palindromic repeats) technology has revolutionized both fundamental research and genomic medicine. The need for precise control of SpCas9-based CRISPR genome editing has led to the development of various strategies to regulate Cas9 activity, aiming to minimize off-target effects. Proteolysis-targeting chimeras (PROTACs) use the ubiquitin-proteasome system to selectively degrade target proteins. Here, we developed CASPROTAC 6, a reversible and cell-permeable PROTAC degrader that directly targets SpCas9 proteins for degradation. The CASPROTAC 6 molecule was derived by linking a known SpCas9 binder BRD7087 with an S-substituted Lenalidomide cereblon (CRBN) ligand via a six-carbon alkyl linker. Our data show that CASPROTAC 6 is a broad-spectrum degrader of SpCas9 and variants such as dCas9 and Cas9 nickases. CASPROTAC 6 degrades SpCas9 and the SpCas9-guide RNA complex via the proteasome system by approximately 50%. As a result, CASPROTAC 6 effectively enhanced the precision of CRISPR/Cas9-mediated genome editing by increasing target specificity. CASPROTAC 6 may serve as modulators of CRISPR/SpCas9-associated nucleases, enabling precise genome editing while reducing off-target effects and enhancing biosafety.

biochemistry↗

bioRxiv2025

Butyrolactol A is a phospholipid flippase inhibitor that potentiates the bioactivity of caspofungin against resistant fungi

Fungal infections cause millions of deaths annually and are challenging to treat due to limited therapeutic options and rising resistance. Cryptococci are intrinsically resistant to the latest generation of antifungals, echinocandins, while Candida auris, a notorious global threat, is also increasingly resistant. We performed a natural product extract screen to rescue caspofungin fungicidal activity against Cryptococcus neoformans H99 and identified butyrolactol A, which restores echinocandin efficacy against resistant fungal pathogens, including multidrug-resistant C. auris. Mode of action studies revealed that butyrolactol A inhibits the phospholipid flippase Apt1-Cdc50, blocking phospholipid transport. Cryo-electron microscopy analysis of the Apt1*butyrolactol A complex revealed that the flippase is trapped in a dead-end state. Apt1 inhibition disrupts membrane asymmetry, vesicular trafficking, and cytoskeletal organization, thereby enhancing echinocandin uptake and potency. This study identifies lipid flippases as promising antifungal targets and demonstrates the potential of revisiting natural products to expand the antifungal arsenal and combat resistance.

biochemistry↗

bioRxiv2024

Accurate de novo design of a voltage-gated anion channel

Ion channels gated by environmental cues play key roles in fundamental biological processes. Designing ion channels with tailored gating mechanisms remains a significant challenge due to the complexities involved in designing conformational changes in proteins. Here we report the accurate de novo design of a voltage-gated anion channel, namely VGAC. VGAC adopts a 15-helix pentameric structure featuring a constriction composed of five arginine residues within the transmembrane span. In patch-clamp experiments, VGAC showed strictly voltage-dependent currents and demonstrated selectivity for chloride anions over iodide anions. Our data suggests that the arginine constriction undergoes voltage-induced conformational changes, serving as both the voltage sensor and selectivity filter. A 2.9-[A]-resolution cryo-electron microscopy structure of VGAC closely aligns with the design model. The ability to design ion channels with custom-designed conformational changes provides new insights into our understanding of the fundamental principles of membrane biophysics and unveils a wide range of potential applications.

synthetic biology↗

bioRxiv2024

Cells Prioritize the Regulation of Cell Mass Density

A cells global physical state is characterized by its volume and dry mass. The ratio of cell mass to volume is the cell mass density (CMD), which is also a measure of macromolecular crowding and concentrations of all proteins. Using the Fluorescence eXclusion method (FXm) and Quantitative Phase Microscopy (QPM), we investigate CMD dynamics after exposure to sudden media osmolarity change. We find that while the cell volume and mass exhibit complex behavior after osmotic shock, CMD follows a straightforward monotonic recovery in 48 hours. The recovery is cell-cycle independent and relies on a coordinated adjustment of protein synthesis and volume growth rates. Surprisingly, we find that the protein synthesis rate decreases when CMD increases. This result is explained by CMD-dependent nucleoplasm-cytoplasm transport, which serves as negative regulatory feedback on CMD. The Na+/H+ exchanger NHE plays a role in regulating CMD by affecting both protein synthesis and volume change. Taken together, we reveal that cells possess a robust control system that actively regulates CMD during environmental change.

biophysics↗